Rinse beans and place them in a large pot with rosemary, and thyme. Cover with water.
Bring to a boil. Reduce heat and gently simmer until beans are tender, about 2 hours.
Drain beans and discard the herbs.
Return beans to pot. Add honey, apples and squash.
Heat olive oil in a small frying pan. Sauté leek and bell pepper in olive oil until tender. Add to bean mixture.
Add a pinch of sage and salt and pepper to taste
Spoon into a 3-quart casserole dish. Add 1 cup of water. Cover and bake at 325 degrees for 60 - 90 minutes or until vegetables are cooked through.